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I got my CycloDS not long ago, and decided to start and convert videos for it (my old ones weren't little-endian, among other things.) So I finally fine-tuned the settings until I got the best possible quality. Unfortunately, that quality really sucks. It keeps jittering every second or so. Incredibly annoying. I know it's not my card (class-6 SDHC, and the DPGtools converted vids work fine.). My settings are currently:
25FPS (I tried 12FPS and it still jitters)
160k vbitrate (192k and 256k are all the same)
44100Hz (anything else and everything sounds really squeaky. LOL)
DPG0 Header + MPEG Layer 1 Video + MPEG Layer 2 Audio
No GOP (no idea how).
64k abitrate (128k makes it stutter more)
Any idea? I am using mencoder for video and ffmpeg for audio. I tried a 2-minute clip, and a 43-minute episode. Both stutter.

Try the DPGconv script, which should help you convert video files in Linux.

I know very little about the DPG file format, but I suspect the use of DPG0 instead of a newer version and the use of 44100Hz audio is probably screwing things up. The framerate of 25 is too high, should probably be closer to 20 or 22 max, but that's a secondary issue IMO.